ot the picture! Here is it!
From: Paul Emsley [pems...@mrc-lmb.cam.ac.uk<mailto:pems...@mrc-lmb.cam.ac.uk>]
Sent: Sunday, September 14, 2014 6:16 PM
To: Wang, Bing
Cc: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] ligand mismathces in pdb deposit
On 12/09
> From: Paul Emsley [pems...@mrc-lmb.cam.ac.uk]
> Sent: Sunday, September 14, 2014 6:16 PM
> To: Wang, Bing
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] ligand mismathces in pdb deposit
>
> On 12/09/14 23:28, Wang, Bing wrote:
> > Hi guys,
>
> Hello.
>
>
Forgot the picture! Here is it!
From: Paul Emsley [pems...@mrc-lmb.cam.ac.uk]
Sent: Sunday, September 14, 2014 6:16 PM
To: Wang, Bing
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ligand mismathces in pdb deposit
On 12/09/14 23:28, Wang, Bing wrote
[pems...@mrc-lmb.cam.ac.uk]
Sent: Sunday, September 14, 2014 6:16 PM
To: Wang, Bing
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ligand mismathces in pdb deposit
On 12/09/14 23:28, Wang, Bing wrote:
> Hi guys,
Hello.
>
> A quick question about pdb deposition! My protein has a common li
On 12/09/14 23:28, Wang, Bing wrote:
Hi guys,
Hello.
A quick question about pdb deposition! My protein has a common ligand
'heme' which mismatches with the ligand in pdb CCD (/Chemical
Component Dictionary/).
What makes you think so?
However i didn't find any differences in it. Is that
1. what is the 3-letter code (residue type) of your heme? Ligand Explorer shows
maybe half a dozen ligands for heme. Most notable HEM (protoporphrin 9 with Fe),
HEC (same but with the double bonds in the vinyl substituents saturated) and
HEA (heme a). There is even an entry for the trypanosomal/Eu
Dear Bing Wang,
To solve your problem, you may try to take a eme ligand directly from a
PDB that contains it, e.g. 1HRC.
You should download the PDB file and to copy and paste the ligand
coordinates in a new file and then use this new pdb file to refine your
structure.
It could be a good s
Hi guys,
A quick question about pdb deposition! My protein has a common ligand 'heme'
which mismatches with the ligand in pdb CCD (Chemical Component Dictionary).
However i didn't find any differences in it. Is that because of the positions
of double bonds or hydrogen atoms, since my model don'
